/** DOCUMENT ME!! */
public float graphMax;
+ /**
+ * Score associated with label and description.
+ */
+ public double score= Double.NaN;
+ /**
+ * flag indicating if annotation has a score.
+ */
+ public boolean hasScore=false;
+
public GraphLine threshold;
// Graphical hints and tips
public int graphHeight = 40;
- public boolean padGaps = true;
+ public boolean padGaps = false;
public static final int NO_GRAPH = 0;
public static final int LINE_GRAPH = 2;
+ public boolean belowAlignment = true;
+
+
public static int getGraphValueFromString(String string)
{
if (string.equalsIgnoreCase("BAR_GRAPH"))
*
* @param label DOCUMENT ME!
* @param description DOCUMENT ME!
- * @param annotations DOCUMENT ME!
+ * @param annotations DOCUMENT ME!about:blank
+Loading...
*/
public AlignmentAnnotation(String label, String description,
Annotation[] annotations)
{
if (annotations[i] == null)
{
- padGaps = false;
continue;
}
-
if (annotations[i].secondaryStructure == 'H' ||
annotations[i].secondaryStructure == 'E')
{
- hasIcons = true;
+ hasIcons = true;
+ }
+
+ if(annotations[i].displayCharacter==null)
+ {
+ continue;
}
if (annotations[i].displayCharacter.length() == 1
&& !annotations[i].displayCharacter.equals("E")
&& !annotations[i].displayCharacter.equals("-")
&& !annotations[i].displayCharacter.equals("."))
- {
- if (jalview.schemes.ResidueProperties.aaIndex
- [annotations[i].displayCharacter.charAt(0)] < 23)
{
- nonSSLabel = true;
+ if (jalview.schemes.ResidueProperties.aaIndex
+ [annotations[i].displayCharacter.charAt(0)] < 23)
+ {
+ nonSSLabel = true;
+ }
}
- }
- if (annotations[i].displayCharacter.length() > 0)
- {
- hasText = true;
+ if (annotations[i].displayCharacter.length() > 0)
+ {
+ hasText = true;
+ }
}
- else
- padGaps = false;
- }
-
if (nonSSLabel)
{
* if appropriate.
*/
private void validateRangeAndDisplay() {
+
+ if (annotations==null)
+ {
+ visible=false; // try to prevent renderer from displaying.
+ return; // this is a non-annotation row annotation - ie a sequence score.
+ }
+
int graphType = graph;
float min = graphMin;
float max = graphMax;
continue;
}
- if (drawValues && annotations[i].displayCharacter.length() > 1)
+ if (drawValues
+ && annotations[i].displayCharacter!=null
+ && annotations[i].displayCharacter.length() > 1)
{
drawValues = false;
}
this.hasText = annotation.hasText;
this.height = annotation.height;
this.label = annotation.label;
+ this.padGaps = annotation.padGaps;
+ this.visible = annotation.visible;
+ if (this.hasScore = annotation.hasScore)
+ {
+ this.score = annotation.score;
+ }
if (threshold!=null) {
threshold = new GraphLine(annotation.threshold);
}
}
for (int i=0; i<ann.length; i++)
{
- if (ann[i]==a)
- {
+ if (ann[i]==a)
+ {
sequenceMapping.put(p, annotations[i]);
}
}
*/
public void restrict(int startRes, int endRes)
{
+ if (startRes<0)
+ startRes=0;
+ if (startRes>=annotations.length)
+ startRes = annotations.length-1;
+ if (endRes>=annotations.length)
+ endRes = annotations.length-1;
+ if (annotations==null)
+ return;
Annotation[] temp = new Annotation[endRes-startRes+1];
- System.arraycopy(annotations, startRes, temp, 0, endRes-startRes+1);
+ if (startRes<annotations.length)
+ {
+ System.arraycopy(annotations, startRes, temp, 0, endRes-startRes+1);
+ }
if (sequenceRef!=null) {
// Clip the mapping, if it exists.
int spos = sequenceRef.findPosition(startRes);
public boolean padAnnotation(int length) {
if (annotations==null)
{
- annotations = new Annotation[length];
- return true;
+ return true; // annotation row is correct - null == not visible and undefined length
}
if (annotations.length<length)
{
return true;
}
return annotations.length>length;
-
+
}
/**
{
return;
}
-
+ sequenceRef=seqRef;
+ if (annotations==null)
+ {
+ return;
+ }
sequenceMapping = new java.util.Hashtable();
- sequenceRef = seqRef;
int seqPos;
for (int i = 0; i < annotations.length; i++)
if (sequenceRef==null)
return;
+ if (annotations==null)
+ {
+ return;
+ }
+
int a = 0, aSize = sequenceRef.getLength();
if (aSize == 0)
* number of non-null annotation elements.
* @return
*/
- private int compactAnnotationArray() {
- int j=0;
- for (int i=0;i<annotations.length; i++) {
- if (annotations[i]!=null && j!=i) {
- annotations[j++] = annotations[i];
+ public int compactAnnotationArray() {
+ int i=0,iSize=annotations.length;
+ while (i<iSize)
+ {
+ if (annotations[i]==null) {
+ if (i+1<iSize)
+ System.arraycopy(annotations, i+1, annotations, i, iSize-i-1);
+ iSize--;
+ } else {
+ i++;
}
}
Annotation[] ann = annotations;
- annotations = new Annotation[j];
- System.arraycopy(ann, 0, annotations, 0, j);
+ annotations = new Annotation[i];
+ System.arraycopy(ann, 0, annotations, 0, i);
ann = null;
- return j;
+ return iSize;
}
/**
sequenceRef = null;
}
}
+
+ /**
+ * @return the score
+ */
+ public double getScore()
+ {
+ return score;
+ }
+
+ /**
+ * @param score the score to set
+ */
+ public void setScore(double score)
+ {
+ hasScore=true;
+ this.score = score;
+ }
+ /**
+ *
+ * @return true if annotation has an associated score
+ */
+ public boolean hasScore()
+ {
+ return hasScore || !Double.isNaN(score);
+ }
+ /**
+ * Score only annotation
+ * @param label
+ * @param description
+ * @param score
+ */
+ public AlignmentAnnotation(String label, String description, double score)
+ {
+ this(label, description, null);
+ setScore(score);
+ }
+
+ public void setPadGaps(boolean padgaps, char gapchar)
+ {
+ this.padGaps = padgaps;
+ if(padgaps)
+ {
+ hasText = true;
+ for(int i=0; i<annotations.length; i++)
+ {
+ if(annotations[i]==null)
+ annotations[i] = new Annotation(String.valueOf(gapchar),null,' ',0f);
+ else if(annotations[i].displayCharacter==null ||annotations[i].displayCharacter.equals(" "))
+ annotations[i].displayCharacter=String.valueOf(gapchar);
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff